Officials of Maine’s Indian tribes are hopeful that the U.S. Environmental Protection Agency’s decision to seek additional help in deciding who should oversee water quality issues on tribal lands means that the federal agency is leaning toward supporting their cause.

The EPA confirmed Tuesday that it had officially accepted Maine’s proposal to issue federal wastewater discharge permits in the vast majority of the state. The agency deferred a decision on who should issue the permits in “Indian country,” and has asked the U.S. Department of Justice to review the matter.

In addition, the EPA said that it would keep a close eye on permits issued by the state to fish farms, because discharges from such facilities could affect wild Atlantic salmon, now an endangered species.

The decision was signed by EPA regional administrator Mindy Lubber on Friday, and it will be published in the Federal Register within a month.

Shortly after Maine applied in 1999 for authority to issue federal wastewater discharge permits under the Clean Water Act, the state’s Indian tribes objected, saying they thought the federal government should retain oversight in tribal territories because the state was too lax.

Maine officials asked for the permitting authority to streamline the current process that requires facilities to have discharge licenses from both the state and federal governments. In 44 other states, federal permits are issued by state environmental departments except in Indian territories.

“I’m pleased, in a way,” Penobscot Nation Gov. Barry Dana said of the EPA decision. “We’re still in the ballgame.”

He interpreted the EPA’s action to mean that the agency was seeking a way to retain jurisdiction in Indian country and was looking to the Justice Department to affirm that.

In other states with Indian territories, the federal government retained authority to issue such permits, but other states do not have an arrangement like that established under the Maine Indian Claims Settlement Act. The 20-year-old agreement, however, is interpreted differently by Maine’s state and tribal officials.

State officials say the document stipulates that Indian tribes are to be treated like municipalities and are subject to state laws and regulations. Tribal officials maintain that the agreement carves out areas, termed “internal tribal matters,” that are to be regulated by tribal law. They say water quality is an internal tribal matter.

The EPA already has asked the U.S. Department of the Interior, which oversees tribal matters nationally, to review the water quality matter. The Interior Department said the federal government should continue to issue permits in Indian country rather than turning that authority over to the state.

While pleased that EPA has sought guidance from the Justice Department, Gov. Dana worries that a department headed by conservative John Ashcroft might not be sympathetic to tribal sovereignty. Ashcroft, a former U.S. senator and Missouri governor and attorney general, is undergoing confirmation hearings in the U.S. Senate, where some Democrats have expressed strong opposition to his nomination.

Because this issue has dragged on for more than a year, the state is eager for a final decision from the EPA. Therefore, officials have denied the federal agency an extension of time to review the matter. The state’s denial, however, doesn’t mean much, and EPA continues to take more time on the issue as it awaits an opinion from the Justice Department. It does mean that neither the EPA nor the DEP can issue permits in the disputed area.

The extension was denied, said Martha Kirkpatrick, the Maine DEP commissioner, to keep the matter in limbo. Otherwise, she said, “it wouldn’t have the urgency it needs.”

“It’s already taken too darn long,” Kirkpatrick said.

The state now has the authority to issue permits to more than 300 facilities that discharge wastewater. Only twenty-two facilities are located in “Indian country.” However, none of these facilities are in need of new or modified permits. If that changes, the state will re-evaluate the situation, Kirkpatrick said.

According to the EPA, Indian country comprises the Passamaquoddy reservation lands at Pleasant Point and Indian Township and tribal trust lands. Only Indian facilities need water discharge permits on these lands.

The Penobscot Nation land is defined as lands surrounding the main stem of the Penobscot River from Indian Island north to where it branches in Medway, the west branch of the river and the Piscataquis and Mattawamkeag tributaries. Dischargers within these areas include the Great Northern mills in Millinocket and East Millinocket, Lincoln Pulp and Paper, and municipal wastewater treatment facilities in Howland, Lincoln and Danforth.

As mandated by the federal Endangered Species Act, EPA had to consult with two federal fisheries agencies to determine whether Atlantic salmon would be harmed by turning permitting authority over to the state. It was determined it would not, but EPA has determined that it will keep a close eye on what is in the permits the state issues to fish farms. Because these operations discharge uneaten food, pesticides and fish waste into the ocean, they need permits.

Two national environmental groups have sued three of the state’s aquaculture operations claiming that they were violating federal clean water regulations, because they did not have discharge permits from the EPA. The companies had applied for such permits, but never received them from the agency before the dispute erupted. EPA gave them permission to operate while the applications were pending.